PMID- 25591325 OWN - NLM STAT- MEDLINE DCOM- 20150714 LR - 20240322 IS - 1471-2105 (Electronic) IS - 1471-2105 (Linking) VI - 16 IP - 1 DP - 2015 Jan 16 TI - YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. PG - 9 LID - 10.1186/s12859-014-0422-y [doi] LID - 9 AB - BACKGROUND: Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. DESCRIPTION: To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica. CONCLUSIONS: YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis of Yersinia. YersiniaBase can be accessed at http://yersinia.um.edu.my . FAU - Tan, Shi Yang AU - Tan SY AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com. AD - Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com. FAU - Dutta, Avirup AU - Dutta A AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. avirupdutta@gmail.com. FAU - Jakubovics, Nicholas S AU - Jakubovics NS AD - Center for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom. nick.jakubovics@ncl.ac.uk. FAU - Ang, Mia Yang AU - Ang MY AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. angmiayang@gmail.com. AD - Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. angmiayang@gmail.com. FAU - Siow, Cheuk Chuen AU - Siow CC AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. cheukchuen@gmail.com. FAU - Mutha, Naresh Vr AU - Mutha NV AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. nareshmvr@gmail.com. FAU - Heydari, Hamed AU - Heydari H AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. heydarihamed@yahoo.com. AD - Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia. heydarihamed@yahoo.com. FAU - Wee, Wei Yee AU - Wee WY AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. gavinwwy89@hotmail.com. AD - Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. gavinwwy89@hotmail.com. FAU - Wong, Guat Jah AU - Wong GJ AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. winnie.my23dna@gmail.com. AD - Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. winnie.my23dna@gmail.com. FAU - Choo, Siew Woh AU - Choo SW AD - Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. lchoo@um.edu.my. AD - Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. lchoo@um.edu.my. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150116 PL - England TA - BMC Bioinformatics JT - BMC bioinformatics JID - 100965194 SB - IM MH - Chromosome Mapping MH - *Databases, Genetic MH - *Genome, Bacterial MH - Genomics/*methods MH - Humans MH - Internet MH - Phylogeny MH - Search Engine MH - *Software MH - User-Computer Interface MH - Virulence/*genetics MH - Yersinia/classification/*genetics/pathogenicity MH - Yersinia Infections/microbiology PMC - PMC4384384 EDAT- 2015/01/17 06:00 MHDA- 2015/07/15 06:00 PMCR- 2015/01/16 CRDT- 2015/01/17 06:00 PHST- 2014/09/12 00:00 [received] PHST- 2014/12/11 00:00 [accepted] PHST- 2015/01/17 06:00 [entrez] PHST- 2015/01/17 06:00 [pubmed] PHST- 2015/07/15 06:00 [medline] PHST- 2015/01/16 00:00 [pmc-release] AID - s12859-014-0422-y [pii] AID - 422 [pii] AID - 10.1186/s12859-014-0422-y [doi] PST - epublish SO - BMC Bioinformatics. 2015 Jan 16;16(1):9. doi: 10.1186/s12859-014-0422-y.